Hi everyone,
When I'm trying to use in my local galaxy HISAT2 for mapping the reads I have an information that reference genome is not available.
I'm interested in grch37. I already downloaded one from Ensembl but I'd like to figure out how to use the one built in HISAT2.
I'd be grateful for help with this issue.
Z.

The final option is to use the genome as a custom reference genome. This uses much more resource than pre-computed indexes and you might run into memory problems, it depends on your configuration. It works well for small genomes (at any server) but even Galaxy Main can produce memory-related tool failures when using very large custom genomes like Human. https://galaxyproject.org/learn/custom-genomes/